Poster Presentation Lorne Infection and Immunity 2020

Identification of novel bacterial species, associated with paediatric inflammatory bowel disease (PIBD), through direct mucosal sampling (#168)

Gemma D'Adamo 1 , Tamblyn Thomason 1 , Jodee Gould 1 , Emily Gulliver 1 , Edward Giles 1 2 , Samuel Forster 1 3
  1. Hudson Institute for Medical Research, Clayton, VICTORIA, Australia
  2. Department of Paediatrics , Monash Health, Melbourne, Victoria, Australia
  3. Wellcome Sanger Institute , CAMBRIDGE, United Kingdom

Inflammatory bowel disease (IBD) is a chronic, incurable condition, comprised of Crohn’s Disease and Ulcerative Colitis. Over 20% of IBD is diagnosed in childhood; however, there are no universally effective treatments and clinical management is complicated by a plethora of side-effects. Until recently, investigation of the microbiota has been limited by an inability to culture the majority of intestinal bacteria. This has led to reliance on microbial sequencing to better understand bacterial community structure; however, sequencing is limited by an inability to unambiguously identify causative bacteria. 

Applying recently developed culturing techniques1, we investigated the microbiota in Paediatric Inflammatory Bowel Disease (PIBD) patients presenting for colonoscopy at Monash Children’s Hospital. Mucosal biopsy samples were collected across three intestinal regions (terminal Ileum, caecum and rectum) in order to characterise microbial signatures among a PIBD cohort. Concurrent bacterial culturing, shotgun metagenomic sequencing and molecular profiling was performed on 175 samples from this paediatric cohort. Bacterial culturing allowed 4546 purified isolates to be archived and identified using 16S rRNA sequencing, with whole genome sequencing performed on 192 of these isolates. Microbial analysis was complemented with examination of the molecular responses initiated at sample sites. RNA-sequencing, combined with qPCR validation of 12 genes of interest (IL6, IL8, IL12, IL17A, IL17F, IL23, CXCL10, TNF-α, STAT3, TREM1, EPCAM, IFN-γ), provided a detailed understanding of the transcriptional responses initiated.  

Reference based metagenomic analysis2 allowed for correlation of the bacterial isolates present with disease states and molecular inflammatory profiles. Future functional characterisation and experimental validation of these isolates will be required to assess their potential roles in disease exacerbation and control. This work will be essential for understanding the role of the microbiome in disease activity and should enable the development of microbiome-based medicines as a therapeutic option for patients with PIBD.

 

1          Browne, H. P. et al. Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation. Nature 533, 543-546 (2016).

2          Forster, S. C. et al. A human gut bacterial genome and culture collection for improved metagenomic analyses.  37, 186 (2019).